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New perspectives on ancient microbes and microbialites: from isotopes to immunology

NEW PERSPECTIVES ON ANCIENT MICROBES AND MICROBIALITES: FROM
ISOTOPES TO IMMUNOLOGY
by
Jake Vincent Bailey
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(EARTH SCIENCES)
August 2008
Copyright 2008 Jake Vincent Bailey

Morphologic data has always played a foundational role in our understanding of ancient life. Visual comparisons often show remarkable similarities between fossils and extant organisms, and yet the modern molecular and geochemical era has taught us that appearances can deceive, and that the genetic and metabolic diversity of the microbial world is greater than anything that could have been previously imagined. What can these revelations in our understanding of the modern microbial biosphere tell us about ancient life, particularly where morphology is conservative?; Sedimentary structures such as stromatolites and winkle structures are often thought to result from the activities of metabolically-complex microbial mat communities. A compound-specific stable isotope approach is used here to analyze nalkanes from Holocene lacustrine stromatolites. Stromatolite-associated n-alkanes are isotopically similar to those is surrounding sediments -- a finding that is perhaps inconsistent with the assumption that metabolically-diverse microbial mat communities were once associated with these structures. Metabolic diversity in microbial mat communities may however, explain the correlation of a particular fossil assemblage with wrinkle structures from the Lower Cambrian Harkless Formation described here.; Fossil cells also provide a window onto the evolution of microbial life. The shape of fossil cells is thought to be an important indicator of their phylogenetic affinities. However, an immunofluorescence and cell biology study of Caulobacter crescentus and its prosthecate relatives suggests that shape-influencing genes may be labile over geologic time scales. Convergent evolution may also result in morphological similarities between distantly-related organisms. Morphologies in modern giant sulfur bacteria are presented that closely resemble abundant globular microfossils from the 600 Ma Doushantuo Formation commonly thought to represent animal embryos. If correct, this reassessment may also explain some lithological and geochemical features of the Neoproterozoic record, such as sulfur isotope excursions and phosphorite proliferation.; Finally, molecular detection methods used to study extant life may also be adapted for the study of ancient life. Monoclonal antibodies allow for the in situ detection of squalane in Eocene-age rocks and suggests the potential to use immunological probes to visualize the distribution of molecular fossils in microfossils, rock fabrics etc.

NEW PERSPECTIVES ON ANCIENT MICROBES AND MICROBIALITES: FROM
ISOTOPES TO IMMUNOLOGY
by
Jake Vincent Bailey
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(EARTH SCIENCES)
August 2008
Copyright 2008 Jake Vincent Bailey